turning off sampled ancestors for FBD analysis

[Jo Baker]

Dear all, 

I have been trying to run a total-evidence FBD witho no sampled ancestors (i.e. making sure we treat all fossils as tips). However, I just wanted to clarify the way to do this with the current implementations of the FBD model and SA being integrated together within BEAUti. 

In order to remove SA from the analysis, I turned the leaf-to-node-jump operator off in the XML. I was not sure whether I also then needed to switch the other tree operators to the non-SA versions.

I copy the original operator specifications and my edits and annotations below - would this be the correct approach?

Many thanks, 

Jo 

        <!--A dimension changing move that jumps between two trees, where a particular sampled node is an ancestor in one tree and a leaf in the other. From Gavryushkina et al (2014) PLOS Biology -->

        <!-- <operator id="LeafToSAFBD.t:fbd_tree" spec="sa.evolution.operators.LeafToSampledAncestorJump" tree="@Tree.t:fbd_tree" weight="10.0"/> -->

        <!-- Turn off this operator-->

        <operator id="LeafToSAFBD.t:fbd_tree" spec="sa.evolution.operators.LeafToSampledAncestorJump" tree="@Tree.t:fbd_tree" weight="0"/>

        <!-- Extension of the Wilson-Balding operator (a type of subtree prune and regraft) that is identical to the original implementation when there are no sampled ancestors.

            Proposes significant changes to a tree including number of nodes. From Gavryushkina et al (2014) PLOS Biology -->

        <!-- <operator id="SAWilsonBaldingFBD.t:fbd_tree" spec="sa.evolution.operators.SAWilsonBalding" tree="@Tree.t:fbd_tree" weight="10.0"/> -->

        <!-- Switch to the non SA version of the operator-->

        <operator id="WilsonBaldingFBD.t:fbd_tree" spec="beast.base.evolution.operator.WilsonBalding" tree="@Tree.t:fbd_tree" weight="10.0"/>

        <!-- Extend narrow and wide exchange operators in BEAST2 to also apply to sampled ancestor trees. Also use a scale operator and uniform operator to propose height changes-->

        <!-- <operator id="SAWideFBD.t:fbd_tree" spec="sa.evolution.operators.SAExchange" isNarrow="false" tree="@Tree.t:fbd_tree" weight="10.0"/>

        <operator id="SANarrowFBD.t:fbd_tree" spec="sa.evolution.operators.SAExchange" tree="@Tree.t:fbd_tree" weight="10.0"/>

        <operator id="SAUniformOperatorFBD.t:fbd_tree" spec="sa.evolution.operators.SAUniform" tree="@Tree.t:fbd_tree" weight="20.0"/>

        <operator id="SATreeRootScalerFBD.t:fbd_tree" spec="sa.evolution.operators.SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:fbd_tree" weight="1.0"/>

        <operator id="SATreeScalerFBD.t:fbd_tree" spec="sa.evolution.operators.SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:fbd_tree" weight="3.0"/> -->

        <!-- Switch to the non-SA version of these operators-->

        <operator id="WideFBD.t:fbd_tree" spec="beast.base.evolution.operator.Exchange" isNarrow="false" tree="@Tree.t:fbd_tree" weight="10.0"/>

        <operator id="NarrowFBD.t:fbd_tree" spec="beast.base.evolution.operator.Exchange" tree="@Tree.t:fbd_tree" weight="10.0"/>

        <operator id="UniformOperatorFBD.t:fbd_tree" spec="beast.base.evolution.operator.Uniform" tree="@Tree.t:fbd_tree" weight="20.0"/>

        <operator id="TreeRootScalerFBD.t:fbd_tree" spec="beast.base.evolution.operator.ScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:fbd_tree" weight="1.0"/>

        <operator id="TreeScalerFBD.t:fbd_tree" spec="beast.base.evolution.operator.ScaleOperator" scaleFactor="0.95" tree="@Tree.t:fbd_tree" weight="3.0"/>